Grants and Contributions:

Grant or Award spanning more than one fiscal year. (2017-2018 to 2018-2019)

The microbial world consists of more than a million species of bacteria that live in a wide variety of environmental niches, including boiling water, extremes of pH, radioactive rocks, and sub-zero sea ice. In order to study a bacterium or exploit its biodiversity for human benefits, microbiologists need to cultivate a bacterium in the laboratory as a pure culture. However, a large proportion of the world’s bacteria are difficult or impossible to cultivate in pure culture.
Despite the difficulty in cultivating many bacteria, the DNA sequences of their genomes is becoming available through the application of “next generation” DNA sequencing techniques. Thus, we can have the DNA sequence of a bacterial genome even when the bacterium has never been cultivated. In this proposal we describe approaches to capturing the genome of any bacterium in a common laboratory strain of E. coli , and subsequently launching the activity of that genome while destroying the host E. coli chromosome, thus switching the species of the organism. This proposal offers a transformation in our ability to study and exploit the benefits of untapped microbial biodiversity.
The research plan for this challenging program is broken up into smaller projects that allow us to develop the technologies needed to achieve our final goal. Such projects include testing in vivo recombination approaches to progressively create a 1Mb BAC and strategies to fuse two 1 Mb BACs using bacterial conjugation and site-specific recombinases. To test our strategy we will use the genome of Thermus thermophilus , which is one of the smallest genomes (~2 Mbp) of free-living bacteria.